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The current samtools view behavior is to extract any read that overlaps with the target region, I wonder if it is possible to add an option to select only reads whose start coordinates fall inside the…
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Hi, when i tried to install arg_oap through code "conda install -c bioconda -c conda-forge args_oap" ,
there are something wrong, as follow:
$ mamba install args_oap
Looking for: ['args_oa…
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Hi,
We still need "wbu" mode for pipe output, such as
bwa | samtools fixmate | samtools sort
but now 'samtools view -u ' is changed from 'wbu' to 'wb0', and the 'wbu' support in the sou…
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Hii,
I installed HLA-LA through conda. I have downloaded graph and indexed, And while running the HLA-LA.pl I am getting below error
Have found no compatible reference specifications in /home/admi…
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I wonder if it is possible to use pipe as input to bismark_methylation_extractor instead of file? something like
samtools view bam.bam|head -1| bismark_methylation_extractor
jksr updated
8 months ago
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hi ，I have ran ALLhic with such error, i do not know how to fix it ,my orders and the error.log are as follow:
bwa index draft.asm.fasta
samtools faidx draft.asm.fasta &
bwa aln -t 10 draft.asm.fa…
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`test/vcf/4.3/passed/complexfile_passed_000.vcf` has an invalid unstructured header line:
https://github.com/samtools/hts-specs/blob/401e2ec3e8ecf19fa89def74e9c27c1e40df341e/test/vcf/4.3/passed/com…
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Hello, Ye Zheng:
Maybe your index.html(https://yezhengstat.github.io/CUTTag_tutorial/index.html) file have some error.
1.In section 3.3, You Wrote 'rmDuplicate' mistakes as 'removeDuplicate'.
2…
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We need to dynamically create a dependency graph based on the input and output files to visualize the progress of the workflows.
Some options we should consider from snakemake
--d3dag, --dag, --ru…
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**Hi everybody,**
**I try to merge .cram files downloaded from EGA. It is impossible to run cramtools-3.**
/storage/software/jdk-1.8.0-25/bin/java -jar /folder/cramtools-3/cramtools/cramtools-3.…